LAMMPS (10 Jan 2012)
# Rhodopsin model

variable	x index 1
variable	y index 1
variable	z index 1

units           real  
neigh_modify    delay 5 every 1   

atom_style      full  
atom_modify	map hash
bond_style      harmonic 
angle_style     charmm 
dihedral_style  charmm 
improper_style  harmonic 
pair_style      lj/charmm/coul/long 8.0 10.0 
pair_modify     mix arithmetic 
kspace_style    pppm 1e-4 

read_data       data.rhodo
  4 = max bonds/atom
  8 = max angles/atom
  18 = max dihedrals/atom
  2 = max impropers/atom
  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
  1 by 2 by 2 MPI processor grid
  32000 atoms
  32000 velocities
  27723 bonds
  40467 angles
  56829 dihedrals
  1034 impropers
  4 = max # of 1-2 neighbors
  12 = max # of 1-3 neighbors
  24 = max # of 1-4 neighbors
  26 = max # of special neighbors

replicate	$x $y $z
replicate	2 $y $z
replicate	2 2 $z
replicate	2 2 1
  orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
  2 by 2 by 1 MPI processor grid
  128000 atoms
  110892 bonds
  161868 angles
  227316 dihedrals
  4136 impropers
  4 = max # of 1-2 neighbors
  12 = max # of 1-3 neighbors
  24 = max # of 1-4 neighbors
  26 = max # of special neighbors

fix             1 all shake 0.0001 5 0 m 1.0 a 232
  6468 = # of size 2 clusters
  14532 = # of size 3 clusters
  2988 = # of size 4 clusters
  16932 = # of frozen angles
fix             2 all npt temp 300.0 300.0 100.0 		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1

special_bonds   charmm
 
thermo          50
thermo_style    multi 
timestep        2.0

run		100
PPPM initialization ...
  G vector = 0.248586
  grid = 48 60 36
  stencil order = 5
  RMS precision = 7.66425e-05
  using double precision FFTs
  brick FFT buffer size/proc = 41615 25920 12915
Memory usage per processor = 146.135 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =   -101425.4826 KinEng   =     85779.3251 Temp     =       299.0304 
PotEng   =   -187204.8077 E_bond   =     10151.9760 E_angle  =     43685.4968 
E_dihed  =     20847.1460 E_impro  =       854.0463 E_vdwl   =     -9231.4537 
E_coul   =    827025.3556 E_long   =  -1080537.3749 Press    =      -142.3084 
Volume   =   1231980.1340 
---------------- Step       50 ----- CPU =     19.1088 (sec) ----------------
TotEng   =   -101320.2612 KinEng   =     86003.4849 Temp     =       299.8118 
PotEng   =   -187323.7461 E_bond   =      9887.1072 E_angle  =     43346.7920 
E_dihed  =     20958.7034 E_impro  =       908.4715 E_vdwl   =     -7973.4456 
E_coul   =    826113.1533 E_long   =  -1080564.5278 Press    =       238.0165 
Volume   =   1232126.1854 
---------------- Step      100 ----- CPU =     39.1056 (sec) ----------------
TotEng   =   -101158.1517 KinEng   =     86355.6231 Temp     =       301.0394 
PotEng   =   -187513.7747 E_bond   =     10272.0700 E_angle  =     43128.6453 
E_dihed  =     20793.9768 E_impro  =       867.0826 E_vdwl   =     -7586.7196 
E_coul   =    825555.5009 E_long   =  -1080544.3307 Press    =        15.2192 
Volume   =   1232535.8453 
Loop time of 39.1057 on 4 procs for 100 steps with 128000 atoms

Pair  time (%) = 27.0353 (69.1339)
Bond  time (%) = 1.5462 (3.9539)
Kspce time (%) = 4.17715 (10.6817)
Neigh time (%) = 4.37974 (11.1997)
Comm  time (%) = 0.208052 (0.532026)
Outpt time (%) = 0.000296533 (0.000758287)
Other time (%) = 1.75896 (4.49797)

FFT time (% of Kspce) = 0.535835 (12.8278)
FFT Gflps 3d (1d only) = 4.46931 11.0706

Nlocal:    32000 ave 32000 max 32000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    47957 ave 47957 max 47957 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 48112468
Ave neighs/atom = 375.879
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
